libSBML Python API  5.10.0
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libsbml.QualModelPlugin Class Reference
Inheritance diagram for libsbml.QualModelPlugin:
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Detailed Description

{qual}

qual Implementation of the 'qual' package extention to the Model construct. The extension of SBML Level 3 Core's Model class is relatively straightforward: the Qualitative Models Package adds two lists, one for holding qualitativeSpecies (ListOfQualitativeSpecies), and the other for holding transitions (ListOfTransitions). The Model element may contain at most one ListOfQualitativeSpecies, which must contain at least one QualitativeSpecies. It may also contain at most one ListOfTransitions which must contain at least one Transition.

Public Member Functions

def addQualitativeSpecies
 
def addTransition
 
def clone
 
def createQualitativeSpecies
 
def createTransition
 
def getElementByMetaId
 
def getElementBySId
 
def getElementNamespace
 
def getLevel
 
def getListOfAllElements
 
def getListOfQualitativeSpecies
 
def getListOfTransitions
 
def getNumQualitativeSpecies
 
def getNumTransitions
 
def getPackageName
 
def getPackageVersion
 
def getParentSBMLObject
 
def getPrefix
 
def getQualitativeSpecies
 
def getSBMLDocument
 
def getTransition
 
def getURI
 
def getVersion
 
def removeQualitativeSpecies
 
def removeTransition
 
def setElementNamespace
 

Member Function Documentation

def libsbml.QualModelPlugin.addQualitativeSpecies (   self,
  args 
)

Python method signature(s):

addQualitativeSpecies(QualModelPlugin self, QualitativeSpecies qualitativeSpecies)   int

Adds a copy of the given QualitativeSpecies object to the list of qual.

Parameters
qualitativeSpeciesthe QualitativeSpecies object to be added to the list of qual.
Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.QualModelPlugin.addTransition (   self,
  args 
)

Python method signature(s):

addTransition(QualModelPlugin self, Transition transition)   int

Adds a copy of the given Transition object to the list of qual.

Parameters
transitionthe Transition object to be added to the list of qual.
Returns
integer value indicating success/failure of the operation. The possible return values are:
def libsbml.QualModelPlugin.clone (   self)

{qual}

qual Implementation of the 'qual' package extention to the Model construct. The extension of SBML Level 3 Core's Model class is relatively straightforward: the Qualitative Models Package adds two lists, one for holding qualitativeSpecies (ListOfQualitativeSpecies), and the other for holding transitions (ListOfTransitions). The Model element may contain at most one ListOfQualitativeSpecies, which must contain at least one QualitativeSpecies. It may also contain at most one ListOfTransitions which must contain at least one Transition. Python method signature(s):

clone(QualModelPlugin self)   QualModelPlugin

Creates and returns a deep copy of this QualModelPlugin object.

Returns
a (deep) copy of this SBase object
def libsbml.QualModelPlugin.createQualitativeSpecies (   self)

Python method signature(s):

createQualitativeSpecies(QualModelPlugin self)   QualitativeSpecies

Creates a new qual object and adds it to the list of qual objects and returns it.

Returns
a newly created QualitativeSpecies object
def libsbml.QualModelPlugin.createTransition (   self)

Python method signature(s):

createTransition(QualModelPlugin self)   Transition

Creates a new qual object and adds it to the list of qual objects and returns it.

Returns
a newly created Transition object
def libsbml.SBasePlugin.getElementByMetaId (   self,
  args 
)
inherited

Python method signature(s):

getElementByMetaId(SBasePlugin self, string metaid)   SBase

Returns the first child element it can find with the given metaid, or None if no such object is found.

Parameters
metaidstring representing the metaid of objects to find
Returns
pointer to the first element found with the given metaid.
def libsbml.SBasePlugin.getElementBySId (   self,
  args 
)
inherited

Python method signature(s):

getElementBySId(SBasePlugin self, string id)   SBase

Returns the first child element found that has the given id in the model-wide SId namespace, or None if no such object is found.

Parameters
idstring representing the id of objects to find
Returns
pointer to the first element found with the given id.
def libsbml.SBasePlugin.getElementNamespace (   self)
inherited

{core}

Representation of a plug-in object of SBML's package extension.

Additional attributes and/or elements of a package extension which are directly contained by some pre-defined element are contained/accessed by SBasePlugin class which is extended by package developers for each extension point. The extension point, which represents an element to be extended, is identified by a combination of a Package name and a typecode of the element, and is represented by SBaseExtensionPoint class.

For example, the layout extension defines <listOfLayouts> element which is directly contained in <model> element of the core package. In the layout package (provided as one of example packages in libSBML-5), the additional element for the model element is implemented as ListOfLayouts class (an SBase derived class) and the object is contained/accessed by a LayoutModelPlugin class (an SBasePlugin derived class).

SBasePlugin class defines basic virtual functions for reading/writing/checking additional attributes and/or top-level elements which should or must be overridden by subclasses like SBase class and its derived classes.

Package developers must implement an SBasePlugin exntended class for each element to be extended (e.g. SBMLDocument, Model, ...) in which additional attributes and/or top-level elements of the package extension are directly contained.

To implement reading/writing functions for attributes and/or top-level elements of the SBsaePlugin extended class, package developers should or must override the corresponding virtual functions below provided in the SBasePlugin class:

  • reading elements :

    1. virtual SBase createObject (XMLInputStream stream)

      This function must be overridden if one or more additional elements are defined.

    2. virtual bool readOtherXML (SBase parentObject, XMLInputStream stream)

      This function should be overridden if elements of annotation, notes, MathML, etc. need to be directly parsed from the given XMLInputStream object.

  • reading attributes (must be overridden if additional attributes are defined) :

    1. virtual void addExpectedAttributes(ExpectedAttributes& attributes)
    2. virtual void readAttributes (XMLAttributes attributes, ExpectedAttributes& expectedAttributes)
  • writing elements (must be overridden if additional elements are defined) :

    1. virtual void writeElements (XMLOutputStream stream)
  • writing attributes :

    1. virtual void writeAttributes (XMLOutputStream stream)

      This function must be overridden if one or more additional attributes are defined.

    2. virtual void writeXMLNS (XMLOutputStream stream)

      This function must be overridden if one or more additional xmlns attributes are defined.

  • checking elements (should be overridden) :

    1. virtual bool hasRequiredElements()

  • checking attributes (should be overridden) :

    1. virtual bool hasRequiredAttributes()

To implement package-specific creating/getting/manipulating functions of the SBasePlugin derived class (e.g., getListOfLayouts(), createLyout(), getLayout(), and etc are implemented in LayoutModelPlugin class of the layout package), package developers must newly implement such functions (as they like) in the derived class.

SBasePlugin class defines other virtual functions of internal implementations such as:

  • virtual void setSBMLDocument(SBMLDocument d)
  • virtual void connectToParent(SBasesbase)
  • virtual void enablePackageInternal(string pkgURI, string pkgPrefix, bool flag)

These functions must be overridden by subclasses in which one or more top-level elements are defined.

For example, the following three SBasePlugin extended classes are implemented in the layout extension:

  1. SBMLDocumentPlugin class for SBMLDocument element

    (SBMLDocumentPlugin class is a common SBasePlugin extended class for SBMLDocument class. Package developers can use this class as-is if no additional elements/attributes (except for required attribute) is needed for the SBMLDocument class in their packages, otherwise package developers must implement a new SBMLDocumentPlugin derived class.)

  2. LayoutModelPlugin class for Model element

    • <listOfLayouts> element is added to Model object.

    • The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)

      • createObject() : (read elements)
      • readOtherXML() : (read elements in annotation of SBML L2)
      • writeElements() : (write elements)

    • The following virtual functions of internal implementations are overridden: (type of arguments and return values are omitted)

      • setSBMLDocument()
      • connectToParent()
      • enablePackageInternal()

    • The following creating/getting/manipulating functions are newly implemented: (type of arguments and return values are omitted)

      • getListOfLayouts()
      • getLayout ()
      • addLayout()
      • createLayout()
      • removeLayout()
      • getNumLayouts()

  3. LayoutSpeciesReferencePlugin class for SpeciesReference element (used only for SBML L2V1)

    • id attribute is internally added to SpeciesReference object only for SBML L2V1

    • The following virtual functions for reading/writing/checking are overridden: (type of arguments and return values are omitted)

      • readOtherXML()
      • writeAttributes()

Python method signature(s):

getElementNamespace(SBasePlugin self)   string

Returns the XML namespace (URI) of the package extension of this plugin object.

Returns
the URI of the package extension of this plugin object.
def libsbml.SBasePlugin.getLevel (   self)
inherited

Python method signature(s):

getLevel(SBasePlugin self)   long

Returns the SBML level of the package extension of this plugin object.

Returns
the SBML level of the package extension of this plugin object.
def libsbml.SBasePlugin.getListOfAllElements (   self,
  filter = None 
)
inherited

Python method signature(s):

getListOfAllElements(SBasePlugin self, ElementFilter filter=None)   SBaseList
getListOfAllElements(SBasePlugin self)   SBaseList

Returns an SBaseList of all child SBase objects, including those nested to an arbitrary depth.

Returns
an SBaseList
def libsbml.QualModelPlugin.getListOfQualitativeSpecies (   self,
  args 
)

Python method signature(s):

getListOfQualitativeSpecies(QualModelPlugin self)   ListOfQualitativeSpecies
getListOfQualitativeSpecies(QualModelPlugin self)   ListOfQualitativeSpecies

Returns the ListOfQualitativeSpecies in this plugin object.

Returns
ListOfQualitativeSpecies object in this plugin object.
def libsbml.QualModelPlugin.getListOfTransitions (   self,
  args 
)

Python method signature(s):

getListOfTransitions(QualModelPlugin self)   ListOfTransitions
getListOfTransitions(QualModelPlugin self)   ListOfTransitions

Returns the ListOfTransitions in this plugin object.

Returns
ListOfTransitions object in this plugin object.
def libsbml.QualModelPlugin.getNumQualitativeSpecies (   self)

Python method signature(s):

getNumQualitativeSpecies(QualModelPlugin self)   long

Returns the number of QualitativeSpecies object in this plugin object.

Returns
the number of QualitativeSpecies object in this plugin object.
def libsbml.QualModelPlugin.getNumTransitions (   self)

Python method signature(s):

getNumTransitions(QualModelPlugin self)   long

Returns the number of Transition object in this plugin object.

Returns
the number of Transition object in this plugin object.
def libsbml.SBasePlugin.getPackageName (   self)
inherited

Python method signature(s):

getPackageName(SBasePlugin self)   string

Returns the package name of this plugin object.

Returns
the package name of this plugin object.
def libsbml.SBasePlugin.getPackageVersion (   self)
inherited

Python method signature(s):

getPackageVersion(SBasePlugin self)   long

Returns the package version of the package extension of this plugin object.

Returns
the package version of the package extension of this plugin object.
def libsbml.SBasePlugin.getParentSBMLObject (   self,
  args 
)
inherited

Python method signature(s):

getParentSBMLObject(SBasePlugin self)   SBase
getParentSBMLObject(SBasePlugin self)   SBase

Returns the parent SBase object to which this plugin object connected.

Returns
the parent SBase object to which this plugin object connected.
def libsbml.SBasePlugin.getPrefix (   self)
inherited

Python method signature(s):

getPrefix(SBasePlugin self)   string

Returns the prefix of the package extension of this plugin object.

Returns
the prefix of the package extension of this plugin object.
def libsbml.QualModelPlugin.getQualitativeSpecies (   self,
  args 
)

Python method signature(s):

getQualitativeSpecies(QualModelPlugin self, long n)   QualitativeSpecies
getQualitativeSpecies(QualModelPlugin self, long n)   QualitativeSpecies
getQualitativeSpecies(QualModelPlugin self, string sid)   QualitativeSpecies
getQualitativeSpecies(QualModelPlugin self, string sid)   QualitativeSpecies

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getQualitativeSpecies(long n)

Returns the QualitativeSpecies object that belongs to the given index. If the index is invalid, None is returned.

Parameters
nthe index number of the QualitativeSpecies to get.
Returns
the nth QualitativeSpecies in the ListOfQualitativeSpecies.

Method variant with the following signature:
getQualitativeSpecies(string sid)

Returns the qualitativeSpecies object based on its identifier.

Parameters
sida string representing the identifier of the QualitativeSpecies to get.
Returns
QualitativeSpecies in the ListOfQualitativeSpecies with the given id or None if no such QualitativeSpecies exists.
See also
getQualitativeSpecies()
getListOfQualitativeSpecies()
def libsbml.SBasePlugin.getSBMLDocument (   self,
  args 
)
inherited

Python method signature(s):

getSBMLDocument(SBasePlugin self)   SBMLDocument
getSBMLDocument(SBasePlugin self)   SBMLDocument

Returns the parent SBMLDocument of this plugin object.

Returns
the parent SBMLDocument object of this plugin object.
def libsbml.QualModelPlugin.getTransition (   self,
  args 
)

Python method signature(s):

getTransition(QualModelPlugin self, long n)   Transition
getTransition(QualModelPlugin self, long n)   Transition
getTransition(QualModelPlugin self, string sid)   Transition
getTransition(QualModelPlugin self, string sid)   Transition

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
getTransition(long n)

Returns the Transition object that belongs to the given index. If the index is invalid, None is returned.

Parameters
nthe index number of the Transition to get.
Returns
the nth Transition in the ListOfTransitions.

Method variant with the following signature:
getTransition(string sid)

Returns the qualitativeSpecies object based on its identifier.

Parameters
sida string representing the identifier of the Transition to get.
Returns
Transition in the ListOfTransitions with the given id or None if no such Transition exists.
See also
getTransition()
getListOfTransitions()
def libsbml.SBasePlugin.getURI (   self)
inherited

Python method signature(s):

getURI(SBasePlugin self)   string

Gets the URI to which this element belongs to. For example, all elements that belong to SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must would have the URI 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

Unlike getElementNamespace, this function first returns the URI for this element by looking into the SBMLNamespaces object of the document with the its package name. if not found it will return the result of getElementNamespace

Returns
the URI this elements
See also
getPackageName()
getElementNamespace()
SBMLDocument.getSBMLNamespaces()
getSBMLDocument()
def libsbml.SBasePlugin.getVersion (   self)
inherited

Python method signature(s):

getVersion(SBasePlugin self)   long

Returns the SBML version of the package extension of this plugin object.

Returns
the SBML version of the package extension of this plugin object.
def libsbml.QualModelPlugin.removeQualitativeSpecies (   self,
  args 
)

Python method signature(s):

removeQualitativeSpecies(QualModelPlugin self, long n)   QualitativeSpecies
removeQualitativeSpecies(QualModelPlugin self, string sid)   QualitativeSpecies

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeQualitativeSpecies(long n)

Removes the nth QualitativeSpecies object from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the QualitativeSpecies object to remove
Returns
the QualitativeSpecies object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.

Method variant with the following signature:
removeQualitativeSpecies(string sid)

Removes the QualitativeSpecies object with the given id attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe id attribute of the QualitativeSpecies object to remove
Returns
the QualitativeSpecies object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.
def libsbml.QualModelPlugin.removeTransition (   self,
  args 
)

Python method signature(s):

removeTransition(QualModelPlugin self, long n)   Transition
removeTransition(QualModelPlugin self, string sid)   Transition

This method has multiple variants that differ in the arguments they accept. Each is described separately below.


Method variant with the following signature:
removeTransition(long n)

Removes the nth Transition object from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
nthe index of the Transition object to remove
Returns
the Transition object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.

Method variant with the following signature:
removeTransition(string sid)

Removes the Transition object with the given id attribute from this plugin object and returns a pointer to it.

The caller owns the returned object and is responsible for deleting it.

Parameters
sidthe id attribute of the Transition object to remove
Returns
the Transition object removed. As mentioned above, the caller owns the returned object. None is returned if the given index is out of range.
def libsbml.SBasePlugin.setElementNamespace (   self,
  args 
)
inherited

Python method signature(s):

setElementNamespace(SBasePlugin self, string uri)   int

Sets the XML namespace to which this element belongs to. For example, all elements that belong to SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/core'; all elements that belong to Layout Extension Version 1 for SBML Level 3 Version 1 Core must set the namespace to 'http://www.sbml.org/sbml/level3/version1/layout/version1/'

Returns
integer value indicating success/failure of the function. The possible values returned by this function are: